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@andrewyb
In my experience with my blog, Google takes duplicate internal content when there is similarity in the urls.
The bad thing is that in this case what google does is index some pages and not index the others.
It would be better a good debugging and assess what are the URLs or keywords that are positioning your site and one option is to perform a 301 redirection.

@jasparcj
many codes of some pages, can be seen as malicious by the Google robot.
Although they are not bad for users, google detects them in another way.
It is best to consult and review those codes.